11-117428322-CG-C

Variant summary

Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP6_Moderate BS2

The NM_020693.4(DSCAML1):c.*5del variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00138 in 1,482,852 control chromosomes in the GnomAD database, including 13 homozygotes. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.0048 (6 hom., cov: 31)
  • Exomes 𝑓: 0.00099 (7 hom.)
• Consequence: DSCAML1 NM_020693.4 3_prime_UTR
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -3.95

Genes affected

DSCAML1 (HGNC:14656): (DS cell adhesion molecule like 1) The protein encoded by this gene is a member of the Ig superfamily of cell adhesion molecules and is involved in neuronal differentiation. The encoded membrane-bound protein localizes to the cell surface, where it forms aggregates that repel neuronal processes of the same cell type. [provided by RefSeq, Sep 2016]

ACMG classification

Verdict is Likely_benign. Variant got -6 ACMG points.

• BP6: Variant 11-117428322-CG-C is Benign according to our data. Variant chr11-117428322-CG-C is described in ClinVar as [Benign]. Clinvar id is 3037184.Status of the report is criteria_provided_single_submitter, 1 stars.
• BS2: High AC in GnomAd at 723 AD gene.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
DSCAML1	NM_020693.4	c.*5del		3_prime_UTR_variant	33/33	ENST00000651296.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
DSCAML1	ENST00000651296.2	c.*5del		3_prime_UTR_variant	33/33		NM_020693.4
DSCAML1	ENST00000321322.6	c.*5del		3_prime_UTR_variant	33/33	1		P1
DSCAML1	ENST00000527706.5	c.*5del		3_prime_UTR_variant	31/31	5
DSCAML1	ENST00000651172.1			downstream_gene_variant				P1

Frequencies

GnomAD3 genomes AF: 0.00475 AC: 723 AN: 152096 Hom.: 6 Cov.: 31

Gnomad AFR AF: 0.0135

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00733

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.0000942

Gnomad MID AF: 0.00949

Gnomad NFE AF: 0.000500

Gnomad OTH AF: 0.00764

GnomAD3 exomes AF: 0.00166 AC: 378 AN: 227122 Hom.: 2 AF XY: 0.00145 AC XY: 181 AN XY: 125108

Gnomad AFR exome AF: 0.0132

Gnomad AMR exome AF: 0.00381

Gnomad ASJ exome AF: 0.00

Gnomad EAS exome AF: 0.00

Gnomad SAS exome AF: 0.0000365

Gnomad FIN exome AF: 0.0000474

Gnomad NFE exome AF: 0.000618

Gnomad OTH exome AF: 0.00327

GnomAD4 exome AF: 0.000994 AC: 1323 AN: 1330638 Hom.: 7 Cov.: 22 AF XY: 0.000948 AC XY: 633 AN XY: 667482

Gnomad4 AFR exome AF: 0.0140

Gnomad4 AMR exome AF: 0.00407

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.0000738

Gnomad4 FIN exome AF: 0.0000384

Gnomad4 NFE exome AF: 0.000576

Gnomad4 OTH exome AF: 0.00231

GnomAD4 genome AF: 0.00478 AC: 728 AN: 152214 Hom.: 6 Cov.: 31 AF XY: 0.00464 AC XY: 345 AN XY: 74420

Gnomad4 AFR AF: 0.0135

Gnomad4 AMR AF: 0.00732

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00

Gnomad4 FIN AF: 0.0000942

Gnomad4 NFE AF: 0.000500

Gnomad4 OTH AF: 0.00756

Alfa AF: 0.00308 Hom.: 0

Bravo AF: 0.00584

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

DSCAML1-related disorder Benign:1

Benign, criteria provided, single submitter

clinical testing

PreventionGenetics, part of Exact Sciences

May 03, 2019

This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -

Computational scores

Source: dbNSFP v4.3

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs202143844; hg19: chr11-117299038;